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KLHL40 Gene

protein-coding   GIFtS: 41
GCID: GC03P042727

Kelch-Like Family Member 40

(Previous names: kelch repeat and BTB (POZ) domain containing 5, kelch-like...)
(Previous symbol: KBTBD5)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Kelch-Like Family Member 401 2     SRYP2 3
KBTBD51 2 3 5     NEM82 5
Kelch Repeat And BTB (POZ) Domain Containing 51 2     SYRP2 5
Nemaline Myopathy Type 81 2     Kelch-Like 40 (Drosophila)1
sarcosynapsin1 2     Kelch-Like Protein 402
Kelch Repeat And BTB Domain-Containing Protein 52 3     Sarcosynapsin3

External Ids:    HGNC: 303721   Entrez Gene: 1313772   Ensembl: ENSG000001571197   OMIM: 6153405   UniProtKB: Q2TBA03   

Export aliases for KLHL40 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for KLHL40 Gene:
This gene encodes a protein containing a BACK domain, a BTB/POZ domain, and 5 Kelch repeats, however, its exact
function is not known. The gene and the multi-domain protein structure are conserved across different taxa,
including primates, rodents, chicken and zebrafish. (provided by RefSeq, Dec 2012)

GeneCards Summary for KLHL40 Gene:
KLHL40 (kelch-like family member 40) is a protein-coding gene. Diseases associated with KLHL40 include nemaline myopathy 8, autosomal recessive, and severe congenital nemaline myopathy. An important paralog of this gene is KLHL21.

UniProtKB/Swiss-Prot: KLH40_HUMAN, Q2TBA0
Function: Required for skeletal muscle development




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NT_022517.19  NC_018914.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for KLHL40
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKLHL40 promoter sequence
   Search Chromatin IP Primers for KLHL40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KLHL40


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p22.1   Ensembl cytogenetic band:  3p22.1   HGNC cytogenetic band: 3p21.33

KLHL40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KLHL40 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P042727:  view genomic region     (about GC identifiers)

Start:
42,727,011 bp from pter      End:
42,734,036 bp from pter
Size:
7,026 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: KLH40_HUMAN, Q2TBA0 (See protein sequence)
Recommended Name: Kelch-like protein 40  
Size: 621 amino acids; 69257 Da
1 PDB 3D structure from and Proteopedia for KLHL40:
4ASC (3D)    
Secondary accessions: Q86SI1 Q96MR2
Alternative splicing: 2 isoforms:  Q2TBA0-1   Q2TBA0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for KLHL40: NX_Q2TBA0

Explore proteomics data for KLHL40 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See KLHL40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689606.2  
    ENSEMBL proteins: 
     ENSP00000287777  

    KLHL40 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    BTBD: BTB/POZ domain containing
    KLHL: Kelch-like

    Selected InterPro protein domains (see all 7):
     IPR006652 Kelch_1
     IPR011333 BTB/POZ_fold
     IPR017096 Kelch-like_gigaxonin-typ
     IPR013069 BTB_POZ
     IPR011705 BACK

    Graphical View of Domain Structure for InterPro Entry Q2TBA0

    ProtoNet protein and cluster: Q2TBA0

    3 Blocks protein domains:
    IPB000210 BTB/POZ domain
    IPB001497 Methylated-DNA-[protein]-cysteine S-methyltransferase
    IPB011705 BTB/Kelch-associated


    UniProtKB/Swiss-Prot: KLH40_HUMAN, Q2TBA0
    Similarity: Contains 1 BACK (BTB/Kelch associated) domain
    Similarity: Contains 1 BTB (POZ) domain
    Similarity: Contains 5 Kelch repeats


    KLHL40 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: KLH40_HUMAN, Q2TBA0
    Function: Required for skeletal muscle development

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    KLHL40 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for KLHL40:
     Increased cell death HMECs cel 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KLHL40
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for KLHL40

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for KLHL40
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for KLHL40

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    KLH40_HUMAN, Q2TBA0: Cytoplasm, myofibril, sarcomere, A band

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030017sarcomere ----
    GO:0031672A band IEA--

    KLHL40 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KLHL40
    Interactions:

        Search GeneGlobe Interaction Network for KLHL40

    4 Interacting proteins for KLHL40 (Q2TBA03) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    AXIN1O151693I2D: score=1 
    AXIN2Q9Y2T13I2D: score=1 
    CSNK1A1P487293I2D: score=1 
    CSNK1EP496743I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--

    KLHL40 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for KLHL40 (KLH40)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for KLHL40 gene: 
    NM_152393.3  

    Unigene Cluster for KLHL40:

    Kelch-like family member 40
    Hs.350288  [show with all ESTs]
    Unigene Representative Sequence: NM_152393
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000287777(uc003clv.1)
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat KLHL40
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    Additional mRNA sequence: 

    AK056577.1 AK291294.1 AK300682.1 AY176040.1 AY177390.1 BC110491.2 

    2 DOTS entries:

    DT.40285996  DT.431001 

    14 AceView cDNA sequences:

    AY176040 F00401 BU101535 AY177390 AK056577 NM_152393 AI274020 AI097070 
    AI659482 F37359 F27785 AI037905 AW445105 AA340789 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    KLHL40 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    KLHL40 Expression
    About this image


    KLHL40 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
     
     Skeletal Muscle (Muscoskeletal System)
    KLHL40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KLHL40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.350288

    UniProtKB/Swiss-Prot: KLH40_HUMAN, Q2TBA0
    Tissue specificity: Highly expressed in fetal (19, 23 and 31 weeks of gestation) and adult skeletal muscle;
    expression levels tend to be higher in fetal compared to postnatal muscles (at protein level). Aslo expressed in
    fetal and adult heart

        Custom PCR Arrays for KLHL40
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KLHL40

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for KLHL40 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Klhl401 , 5 kelch repeat and BTB (POZ) domain containing 55
    kelch-like 401
    86.75(n)1
    92.73(a)1
      9 (72.61 cM)5
    723301  NM_028202.31  NP_082478.11 
     1217776075 
    chicken
    (Gallus gallus)
    Aves KBTBD51 kelch repeat and BTB (POZ) domain containing 5 70.77(n)
    71.8(a)
      420389  XM_418495.3  XP_418495.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 3)
    Uncharacterized protein
    (see all 3)
    69(a)
    65(a)
    (see all 3)
    1 ↔ many
    1 ↔ many
    (see all 3)
    AAWZ02040060(1652-6291)
    6(2721074-2733208)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia klhl401 kelch-like family member 40 66.72(n)
    68.14(a)
      548534  NM_001015817.1  NP_001015817.1 
    zebrafish
    (Danio rerio)
    Actinopterygii klhl40a1 kelch-like 40a (Drosophila) 61.89(n)
    59.31(a)
      553257  NM_001128682.1  NP_001122154.1 


    ENSEMBL Gene Tree for KLHL40 (if available)
    TreeFam Gene Tree for KLHL40 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KLHL40 gene
    KLHL212  KLHL62  KBTBD82  KLHL412  KBTBD122  KBTBD22  KLHL242  ENC12  
    KLHL382  KLHL292  KBTBD32  KLHL232  KBTBD72  KLHL302  KBTBD62  KLHL252  
    KLHL352  
    3 SIMAP similar genes for KLHL40 using alignment to 1 protein entry:     KLH40_HUMAN:
    BBS5    KLHL41    SARCOSIN

    KLHL40 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for KLHL40 (see all 326)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0698464
    Nemaline myopathy 8 (NEM8)4--see VAR_0698462 A P mis40--------
    VAR_0698384
    Nemaline myopathy 8 (NEM8)4--see VAR_0698382 V E mis40--------
    VAR_0698474
    Nemaline myopathy 8 (NEM8)4--see VAR_0698472 E K mis40--------
    VAR_0698374
    Nemaline myopathy 8 (NEM8)4--see VAR_0698372 L P mis40--------
    VAR_0698364
    Nemaline myopathy 8 (NEM8)4--see VAR_0698362 D H mis40--------
    VAR_0698424
    Nemaline myopathy 8 (NEM8)4--see VAR_0698422 H R mis40--------
    VAR_0698404
    Nemaline myopathy 8 (NEM8)4--see VAR_0698402 R L mis40--------
    VAR_0698434
    Nemaline myopathy 8 (NEM8)4--see VAR_0698432 G C mis40--------
    VAR_0698454
    Nemaline myopathy 8 (NEM8)4--see VAR_0698452 E K mis40--------
    VAR_0698414
    Nemaline myopathy 8 (NEM8)4--see VAR_0698412 P L mis40--------

    HapMap Linkage Disequilibrium report for KLHL40 (42727011 - 42734036 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for KLHL40: --
    Human Gene Mutation Database (HGMD): KLHL40
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KLHL40
    DNA2.0 Custom Variant and Variant Library Synthesis for KLHL40

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 615340   
    OMIM disorders: 615348  
    UniProtKB/Swiss-Prot: KLH40_HUMAN, Q2TBA0
  • Nemaline myopathy 8 (NEM8) [MIM:615348]: A severe form of nemaline myopathy. Nemaline myopathies are
    muscular disorders characterized by muscle weakness of varying severity and onset, and abnormal thread-like or
    rod-shaped structures in muscle fibers on histologic examination. NEM8 is characterized by fetal akinesia or
    hypokinesia, followed by contractures, fractures, respiratory failure, and swallowing difficulties apparent at
    birth. Most patients die in infancy. Skeletal muscle biopsy shows numerous small nemaline bodies, often with no
    normal myofibrils. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 4 diseases for KLHL40:    
    About MalaCards
    nemaline myopathy 8, autosomal recessive    severe congenital nemaline myopathy    nemaline myopathy    myopathy


    KLHL40 for disorders           About GeneDecksing


    Export disorders for KLHL40 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for KLHL40 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with KLHL40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy. (PubMed id 23746549)1, 2, 3 Ravenscroft G....Laing N.G. (Am. J. Hum. Genet. 2013)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Update on the Kelch-like (KLHL) gene family. (PubMed id 23676014)1 Dhanoa B.S....Friedman J.S. (Hum. Genomics 2013)
    5. Structural basis for Cul3 assembly with the BTB-Kelch family of E3 ubiquitin ligases. (PubMed id 23349464)2 Canning P.... Bullock A.N. (J. Biol. Chem. 2013)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    7. (PubMed id )2 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 131377 HGNC: 30372 AceView: KBTBD5 Ensembl:ENSG00000157119 euGenes: HUgn131377
    ECgene: KLHL40 H-InvDB: KLHL40

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for KLHL40 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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